Caron Laboratory
This analysis characterizes post-translational modifications (PTMs) identified on HLA class I peptides from the JY cell line using data-dependent acquisition mass spectrometry. All analyses are restricted to peptides of length 8-14 amino acids.
HLA Alleles: A\*02:01, B\*07:02, C\*07:02
| Dataset | Peptides |
|---|---|
| Background (unmodified) | 77,100 |
| **Total Modified** | **8,804** |
| Cysteinylation | 2,355 |
| Deamidation | 2,081 |
| Oxidation | 1,640 |
| Phosphorylation | 702 |
| Acetylation | 510 |
| Methylation | 475 |
| Ubiquitination | 426 |
| Dimethylation | 319 |
| Citrullination | 250 |
| N-Glycosylation | 42 |
| SUMOylation | 4 |
| PTM Type | Target Residues |
|---|---|
| Phosphorylation | S, T, Y |
| Acetylation | K, N-terminus |
| Cysteinylation | C |
| Methylation | K, R |
| Dimethylation | K, R |
| Deamidation | N, Q |
| Biological Oxidation | P, I, L, Q, S, T, V, C, D, E, N, Y, G, K, R |
| Citrullination | R |
| Ubiquitination | K |
| N-Glycosylation | N |
| SUMOylation | K |
| Category | EL Rank Threshold |
|---|---|
| Strong binder | < 0.5% |
| Weak binder | 0.5% – 2% |
| Non-binder | ≥ 2% |
Distribution of unique modified peptides by PTM type (length 8-14 amino acids).
Proportional representation of each PTM class within the modified peptidome.
Ridgeline density plot comparing peptide length distributions across PTM types. Gray distribution represents unmodified background peptides.
Circos diagram illustrating relationships between PTM types (outer sectors), modified residues (links), and HLA binding alleles (inner elements). Link density reflects relative abundance of each PTM-residue combination.
Log₂ enrichment of PTM occurrence at peptide positions 8-14 relative to background amino acid positional distribution. PTM+residue combinations with ≥20 occurrences. Color scale: blue (depletion) to red (enrichment), capped at ±3. Correlation column indicates similarity to background distribution.
Aggregated positional enrichment by PTM type (≥50 occurrences), combining all modified residues.
Density curves showing modification site distribution across peptide positions 8-14. PTM+residue combinations with ≥50 modifications.
Percentage of strong HLA binders (EL Rank < 0.5%) for each PTM+residue combination across alleles A0201, B0702, and C0702. Combinations with ≥10 peptides.
Percentage of weak HLA binders (0.5% ≤ EL Rank < 2%) for each PTM+residue combination.
Strong binder percentages aggregated by PTM type across alleles.
Weak binder percentages aggregated by PTM type.
EL Rank distribution comparison between modified peptides (colored outlines) and background unmodified peptides (gray) within the binder range (EL Rank 0-2). Dashed lines indicate strong binder (0.5%) and weak binder (2%) thresholds.
Site distribution for peptides carrying two or more phosphorylation sites.
Comparison of ubiquitin remnant types following tryptic digestion: single glycine (G, +57 Da) versus diglycine (GG, +114 Da).
Classification of oxidized peptides: biological oxidation (P, I, L, Q, S, T, V, C, D, E, N, Y, G, K, R) versus artifact oxidation (M, W, H).
HLA binding classification for biologically oxidized peptides stratified by oxidized residue. Sorted by percentage of strong binders.
Strong binder percentages for biological oxidation cross-tabulated by residue and HLA allele.
N-glycosylation analysis stratified by glycan complexity (sum of monosaccharide units). Categories: Simple (1-3), Medium (4-8), Complex (9-15).
Individual glycan structures with HLA binding classification, sorted by monosaccharide count.
Analysis Date: January 2026 | Made by: Peter Kubiniok